I created a system of custom taxonomies and custom post types to hold all of the audit answers in an organized structure. Answers to the audit were saved in a custom table which was perfectly designed to be easy to search and easy to update. I also captured some custom user data, which was linked to the audit to avoid showing inappropriate questions to users (e.g. don't judge an organization's electricity use if they don't have a building). Users were of course forced to log in to take the audit, but visitors were allowed to preview the audit, which has an organized navigation system and colorful bars to track progress and score.
The resources were also a custom post type, tied into the audit with the same taxonomies. All of this functionality was encased in a standalone plugin that could be implemented with any theme.
Once the system was built, I also created a custom import tool so that my client could create a complex spreadsheet of the entire audit, and do a single import to have the whole thing easily loaded into the WordPress database. I also create a few different custom exports to allow them to extract data in spreadsheets for further analysis.